Transcriptome analysis of a subtropical deciduous tree: Autumn leaf senescence gene expression profile of formosan gum

Plant and Cell Physiology

Volumn 56, Issue 1, 2015, Pages 163-174

  Wen, Chi Hsiang ^a   Lin, Shih Shun ^a,b   Chu, Fang Hua ^a  

^a NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^b AGRICULTURAL BIOTECHNOLOGY RESEARCH CENTER   (Taiwan)

Author keywords

Formosan gum; Leaf senescence; Liquidambar formosana; Microarray; Next generation sequencing; Transcriptome

Indexed keywords

LIQUIDAMBAR FORMOSANA;

TRANSCRIPTOME;

COLOR; COMPARATIVE STUDY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HIGH THROUGHPUT SEQUENCING; LIQUIDAMBAR; MICROARRAY ANALYSIS; PHYSIOLOGY; PIGMENTATION; PLANT LEAF; SEASON; TREE;

COLOR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; LIQUIDAMBAR; MICROARRAY ANALYSIS; PIGMENTATION; PLANT LEAVES; SEASONS; TRANSCRIPTOME; TREES;

EID: 84922608911     PISSN: 00320781     EISSN: 14719053     Source Type: Journal    
DOI: 10.1093/pcp/pcu160     Document Type: Article

References (53)

1. Albert, N.W., Davies, K.M., Lewis, D.H., Zhang, H., Montefiori, M., Brendolise, C. et al. (2014) A conserved network of transcriptional activators and repressors regulates anthocyanin pigmentation in eudicots. Plant Cell 26: 962-980.
2. Archetti, M., Döring, T.F., Hagen, S.B., Hughes, N.M., Leather, S.R., Lee, D.W. et al. (2009) Unravelling the evolution of autumn colours: an interdisciplinary approach. Trends Ecol. Evol. 24: 166-173.
3. Aubry, S., Mani, J. and Hörtensteiner, S. (2008) Stay-green protein, defective in Mendel's green cotyledon mutant, acts independent and upstream of pheophorbide a oxygenase in the chlorophyll catabolic pathway. Plant Mol. Biol. 67: 243-256.
4. Bastian, M. and Heymann, S. (2009) Gephi: an open source software for exploring and manipulating networks. International AAAI Conference on Weblogs and Social Media.
5. Besseau, S., Li, J. and Palva, E.T. (2012) WRKY54 and WRKY70 co-operate as negative regulators of leaf senescence in Arabidopsis thaliana. J. Exp. Bot. 63: 2667-2679.
6. Breeze, E., Harrison, E., McHattie, S., Hughes, L., Hickman, R., Hill, C. et al. (2011) High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation. Plant Cell 23: 873-894.
7. Buchanan-Wollaston, V. (1997) The molecular biology of leaf senescence. J. Exp. Bot. 48: 181-199.
8. Büchert, A.M., Civello, P.M. and Martínez, G.A. (2011) Chlorophyllase versus pheophytinase as candidates for chlorophyll dephytilation during senescence of broccoli. J. Plant Physiol. 168: 337-343.
9. Butelli, E., Licciardello, C., Zhang, Y., Liu, J., Mackay, S., Bailey, P. et al. (2012) Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges. Plant Cell 24: 1242-1255.
10. Chang, S., Puryear, J. and Cairney, J. (1993) A simple and efficient method for isolating RNA from pine trees. Plant Mol. Biol. Rep. 11: 113-116.
11. Chung, D.W., Pruzinská, A., Hörtensteiner, S. and Ort, D.R. (2006) The role of pheophorbide a oxygenase expression and activity in the canola green seed problem. Plant Physiol. 142: 88-97.
12. Conesa, A., Götz, S., Garćia-Gómez, J.M., Terol, J., Talón, M. and Robles, M. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676.
13. Contento, A.L., Kim, S. and Bassham, D.C. (2004) Transcriptome profiling of the response of Arabidopsis suspension culture cells to Suc starvation. Plant Physiol. 135: 2330-2347.
14. Devaiah, B.N., Karthikeyan, A.S. and Raghothama, K.G. (2007) WRKY75 transcription factor is a modulator of phosphate acquisition and root development in Arabidopsis. Plant Physiol. 143: 1789-1801.
15. Dubos, C., Stracke, R., Grotewold, E., Weisshaar, B., Martin, C. and Lepiniec, L. (2010) MYB transcription factors in Arabidopsis. Trends Plant Sci. 15: 573-581.
16. Feild, T.S., Lee, D.W. and Holbrook, N.M. (2001) Why leaves turn red in autumn. The role of anthocyanins in senescing leaves of red-osier dogwood. Plant Physiol. 127: 566-574.
17. Gonzalez, A., Zhao, M., Leavitt, J.M. and Lloyd, A.M. (2008) Regulation of the anthocyanin biosynthetic pathway by the TTG1/bHLH/Myb transcriptional complex in Arabidopsis seedlings. Plant J. 53: 814-827.
18. Gould, K.S., Markham, K.R., Smith, R.H. and Goris, J.J. (2000) Functional role of anthocyanins in the leaves of Quintinia serrata Cunn. A. J. Exp. Bot. 51: 1107-1115.
19. Heyman, J., Cools, T., Vandenbussche, F., Heyndrickx, K.S., Van Leene, J., Vercauteren, I. et al. (2013) ERF115 controls root quiescent center cell division and stem cell replenishment. Science 342: 860-863.
20. Hoch, W.A., Zeldin, E.L. and McCown, B.H. (2001) Physiological significance of anthocyanins during autumnal leaf senescence. Tree Physiol. 21: 1-8.
21. Hörtensteiner, S. (2013) Update on the biochemistry of chlorophyll breakdown. Plant Mol. Biol. 82: 505-517.
22. Ishikura, N. (1972) Anthocyanin and other phenolics in autumn leaves. Phytochemistry 11: 2555-2558.
23. Jaakola, L. (2013) New insights into the regulation of anthocyanin biosynthesis in fruits. Trends Plant Sci. 18: 477-483.
24. Jain, M. (2012) Next-generation sequencing technologies for gene expression profiling in plants. Brief. Funct. Genomics 11: 63-70.
25. Jones-Rhoades, M.W., Bartel, D.P. and Bartel, B. (2006) MicroRNAs and their regulatory roles in plants. Annu. Rev. Plant Biol. 57: 19-53.
26. Kaida, R., Serada, S., Norioka, N., Norioka, S., Neumetzler, L., Pauly, M. et al. (2010) Potential role for purple acid phosphatase in the dephosphor-ylation of wall proteins in tobacco cells. Plant Physiol. 153: 603-610.
27. Keskitalo, J., Bergquist, G., Gardeström, P. and Jansson, S. (2005) A cellular timetable of autumn senescence. Plant Physiol. 139: 1635-1648.
28. Kim, J.H., Woo, H.R., Kim, J., Lim, P.O., Lee, I.C., Choi, S.H. et al. (2009) Trifurcate feed-forward regulation of age-dependent cell death involving miR164 in Arabidopsis. Science 323: 1053-1057.
29. 3 during leaf maturation and senescence. Environ. Pollut. 158: 959-968.
30. Krost, C, Petersen, R., Lokan, S., Brauksiepe, B., Braun, P. and Schmidt, E.R (2013) Evaluation of the hormonal state of columnar apple trees (Malu xdomestica) based on high throughput gene expression studies. Plant Mol. Biol. 81: 211-220.
31. Lee, D.W., O'Keefe, J., Holbrook, N.M. and Feild, T.S. (2003) Pigment dynamics and autumn leaf senescence in a New England deciduous forest, eastern USA. Ecol. Res. 18: 677-694.
32. Li, Y.-Y., Mao, K., Zhao, C, Zhao, X.Y., Zhang, H.L, Shu, H.R et al. (2012) MdCOP1 ubiquitin E3 ligases interact with MdMYB1 to regulate light-induced anthocyanin biosynthesis and red fruit coloration in apple. Plant Physiol. 160: 1011-1022.
33. Lim, P.O., Woo, H.R. and Nam, H.G. (2003) Molecular genetics of leaf senescence in Arabidopsis. Trends Plant Sci. 8: 272-278.
34. Lin-Wang, K., Bolitho, K., Grafton, K., Kortstee, A., Karunairetnam, S., McGhie, T.K. et al. (2010) An R2R3 MYB transcription factor associated with regulation of the anthocyanin biosynthetic pathway in Rosaceae. BMC Plant Biol. 10: 50.
35. Lin-Wang, K., Micheletti, D., Palmer, J., Volz, R, Lozano, L, Espley, R. et al. (2011) High temperature reduces apple fruit colour via modulation of the anthocyanin regulatory complex. Plant Cell Environ. 34: 1176-1190.
36. Liu, L-Y.D., Tseng, H.-I., Lin, C.-P., Lin, Y.Y., Huang, Y.H., Huang, CK. et al. (2014) High-throughput transcriptome analysis of the leafy flower transition of Catharanthus roseus induced by peanut witches'-broom phytoplasma infection. Plant Cell Physiol. 55: 942-957.
37. Matile, P. (2000) Biochemistry of Indian summer: physiology of autumnal leaf coloration. Exp. Gerontol. 35: 145-158.
38. McWilliam, H., Li, W., Uludag, M., Squizzato, S., Park Y.M., Buso, N. et al. (2013) Analysis tool web services from the EMBL-EBI. Nucleic Acids Res. 41: W597-W600.
39. Mu, H., Lin, L, Liu, G. and Jiang, J. (2013) Transcriptomic analysis of incised leaf-shape determination in birch. Gene 531: 263-269.
40. Nam, H. (1997) The molecular genetic analysis of leaf senescence. Curr. Opin. Biotechnol. 8: 200-207.
41. Neale, D.B. and Kremer, A. (2011) Forest tree genomics: growing resources and applications. Nat. Rev. Genet. 12: 111-122.
42. Ougham, H.J., Morris, P. and Thomas, H. (2005) The colors of autumn leaves as symptoms of cellular recycling and defenses against environmental stresses. Curr. Top. Dev. Biol. 66: 135-160.
43. Pruzinska, A., Tanner, G, Anders, I., Roca, M. and Hortensteiner, S. (2003) Chlorophyll breakdown: pheophorbide a oxygenase is a Rieske-type iron-sulfur protein, encoded by the accelerated cell death 1 gene. Proc. Natl Acad. Sci. USA 100: 15259-15264.
44. Qiu, Z., Wan, L, Chen, T., Wan, Y., He, X., Lu, S. et al. (2013) The regulation of cambial activity in Chinese fir (Cunninghamia lanceolata) involves extensive transcriptome remodeling. New Phytol. 199: 708-719.
45. Sakuraba, Y., Schelbert, S., Park S.-Y., Han, S.H., Lee, B.D., Andres, C.B. et al. (2012) STAY-GREEN and chlorophyll catabolic enzymes interact at light-harvesting complex II for chlorophyll detoxification during leaf senescence in Arabidopsis. Plant Cell 24: 507-518.
46. Sarwat, M., Naqvi, A.R, Ahmad, P., Ashraf, M. and Akram, N.A. (2013) Phytohormones and microRNAs as sensors and regulators of leaf senescence: assigning macro roles to small molecules. Biotechnol. Adv. 31: 1153-1171.
47. Schaberg, P.G, Murakami, P.F., Turner, M.R, Heitz, H.K. and Hawley, G.J. (2008) Association of red coloration with senescence of sugar maple leaves in autumn. Trees 22: 573-578.
48. Schelbert, S., Aubry, S., Burla, B., Agne, B., Kessler, F., Krupinska, K. et al. (2009) Pheophytin pheophorbide hydrolase (pheophytinase) is involved in chlorophyll breakdown during leaf senescence in Arabidopsis. Plant Cell 21: 767-785.
49. Tanaka, A. and Tanaka, R. (2006) Chlorophyll metabolism. Curr. Opin. Plant Biol. 9: 248-255.
50. Timperio, A.M., Egidi, M.G. and Zolla, L. (2008) Proteomics applied on plant abiotic stresses: role of heat shock proteins (HSP). J. Proteomics 71: 391-411.
51. Winkel-Shirley, B. (2001) Flavonoid biosynthesis. A colorful model for genetics, biochemistry, cell biology, and biotechnology. Plant Physiol. 126: 485-493.
52. Woo, H.R., Kim, H.J., Nam, H.G. and Lim, P.O. (2013) Plant leaf senescence and death-regulation by multiple layers of control and implications for aging in general. J. Cell Sci. 126: 4823-4833.
53. Xu, F., Cheng, H., Cai, R., Li, L.L., Chang, J., Zhu, J. et al. (2008) Molecular cloning and function analysis of an anthocyanidin synthase gene from Ginkgo biloba, and its expression in abiotic stress responses. Mol. Cells 26: 536-547.